@apollo-annotation/cli 0.1.10

package/README.md

@@ -0,0 +1,899 @@
+# Table of contents
+
+<!-- toc -->
+* [Table of contents](#table-of-contents)
+* [Usage](#usage)
+* [Commands](#commands)
+<!-- tocstop -->
+
+# Usage
+
+<!-- usage -->
+```sh-session
+$ npm install -g @apollo-annotation/cli
+$ apollo COMMAND
+running command...
+$ apollo (--version)
+@apollo-annotation/cli/0.1.10 linux-x64 node-v18.20.3
+$ apollo --help [COMMAND]
+USAGE
+  $ apollo COMMAND
+...
+```
+<!-- usagestop -->
+
+# Commands
+
+<!-- commands -->
+* [`apollo assembly add-fasta`](#apollo-assembly-add-fasta)
+* [`apollo assembly add-gff`](#apollo-assembly-add-gff)
+* [`apollo assembly check`](#apollo-assembly-check)
+* [`apollo assembly delete`](#apollo-assembly-delete)
+* [`apollo assembly get`](#apollo-assembly-get)
+* [`apollo assembly sequence`](#apollo-assembly-sequence)
+* [`apollo change get`](#apollo-change-get)
+* [`apollo config [KEY] [VALUE]`](#apollo-config-key-value)
+* [`apollo feature add-child`](#apollo-feature-add-child)
+* [`apollo feature check`](#apollo-feature-check)
+* [`apollo feature copy`](#apollo-feature-copy)
+* [`apollo feature delete`](#apollo-feature-delete)
+* [`apollo feature edit`](#apollo-feature-edit)
+* [`apollo feature edit-attribute`](#apollo-feature-edit-attribute)
+* [`apollo feature edit-coords`](#apollo-feature-edit-coords)
+* [`apollo feature edit-type`](#apollo-feature-edit-type)
+* [`apollo feature get`](#apollo-feature-get)
+* [`apollo feature get-id`](#apollo-feature-get-id)
+* [`apollo feature import`](#apollo-feature-import)
+* [`apollo feature search`](#apollo-feature-search)
+* [`apollo help [COMMANDS]`](#apollo-help-commands)
+* [`apollo login`](#apollo-login)
+* [`apollo logout`](#apollo-logout)
+* [`apollo refseq get`](#apollo-refseq-get)
+* [`apollo status`](#apollo-status)
+* [`apollo user get`](#apollo-user-get)
+
+## `apollo assembly add-fasta`
+
+Add new assembly from local or external fasta file
+
+```
+USAGE
+  $ apollo assembly add-fasta -i <value> [--profile <value>] [--config-file <value>] [-a <value>] [-x <value>] [-f]
+
+FLAGS
+  -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
+  -f, --force                Delete existing assembly, if it exists
+  -i, --input-file=<value>   (required) Input fasta file
+  -x, --index=<value>        URL of the index. Required if input is an external source and ignored if input is a local
+                             file
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Add new assembly from local or external fasta file
+
+EXAMPLES
+  From local file:
+
+    $ apollo assembly add-fasta -i genome.fa -a myAssembly
+
+  From external source we also need the URL of the index:
+
+    $ apollo assembly add-fasta -i https://.../genome.fa -x https://.../genome.fa.fai -a myAssembly
+```
+
+_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
+
+## `apollo assembly add-gff`
+
+Add new assembly from gff or gft file
+
+```
+USAGE
+  $ apollo assembly add-gff -i <value> [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]
+
+FLAGS
+  -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
+  -f, --force                Delete existing assembly, if it exists
+  -i, --input-file=<value>   (required) Input gff or gtf file
+  -o, --omit-features        Do not import features, only upload the sequences
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Add new assembly from gff or gft file
+
+  The gff file is expected to contain sequences as per gff specifications.
+  Features are also imported by default.
+
+EXAMPLES
+  Import sequences and features:
+
+    $ apollo assembly add-gff -i genome.gff -a myAssembly
+
+  Import sequences only:
+
+    $ apollo assembly add-gff -i genome.gff -a myAssembly -o
+```
+
+_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
+
+## `apollo assembly check`
+
+Add, view, or delete checks to assembly
+
+```
+USAGE
+  $ apollo assembly check [--profile <value>] [--config-file <value>] [-a <value>] [-c <value>] [-d]
+
+FLAGS
+  -a, --assembly=<value>     Manage checks in this assembly
+  -c, --check=<value>...     Add these check names or IDs. If unset, print the checks set for assembly
+  -d, --delete               Delete (instead of adding) checks
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Add, view, or delete checks to assembly
+
+  Manage checks, i.e. the rules ensuring features in an assembly are plausible.
+  This command only sets the check to apply, to retrieve features flagged by these
+  checks use `apollo feature check`.
+
+EXAMPLES
+  View available check types:
+
+    $ apollo assembly check
+
+  View checks set for assembly hg19:
+
+    $ apollo assembly check -a hg19
+
+  Add checks to assembly:
+
+    $ apollo assembly check -a hg19 -c CDSCheck
+
+  Delete checks from assembly:
+
+    $ apollo assembly check -a hg19 -c CDSCheck --delete
+```
+
+_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/assembly/check.ts)_
+
+## `apollo assembly delete`
+
+Delete assemblies
+
+```
+USAGE
+  $ apollo assembly delete -a <value> [--profile <value>] [--config-file <value>] [-v]
+
+FLAGS
+  -a, --assembly=<value>...  (required) Assembly names or IDs to delete
+  -v, --verbose              Print to stdout the array of assemblies deleted
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Delete assemblies
+
+  Assemblies to delete may be names or IDs
+
+EXAMPLES
+  Delete multiple assemblies using name or ID:
+
+    $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f
+```
+
+_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/assembly/delete.ts)_
+
+## `apollo assembly get`
+
+Get available assemblies
+
+```
+USAGE
+  $ apollo assembly get [--profile <value>] [--config-file <value>] [-a <value>]
+
+FLAGS
+  -a, --assembly=<value>...  Get assemblies in this list of names or IDs
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get available assemblies
+
+  Print to stdout the list of assemblies in json format
+```
+
+_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/assembly/get.ts)_
+
+## `apollo assembly sequence`
+
+Get reference sequence in fasta format
+
+```
+USAGE
+  $ apollo assembly sequence [--profile <value>] [--config-file <value>] [-a <value>] [-r <value>] [-s <value>] [-e
+    <value>]
+
+FLAGS
+  -a, --assembly=<value>     Find input reference sequence in this assembly
+  -e, --end=<value>          End coordinate
+  -r, --refseq=<value>       Reference sequence. If unset, get all sequences
+  -s, --start=<value>        [default: 1] Start coordinate (1-based)
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get reference sequence in fasta format
+
+  Return the reference sequence for a given assembly and coordinates
+
+EXAMPLES
+  Get all sequences in myAssembly:
+
+    $ apollo assembly sequence -a myAssembly
+
+  Get sequence in coordinates chr1:1..1000:
+
+    $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000
+```
+
+_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+
+## `apollo change get`
+
+Get list of changes
+
+```
+USAGE
+  $ apollo change get [--profile <value>] [--config-file <value>] [-a <value>]
+
+FLAGS
+  -a, --assembly=<value>...  Get changes only for these assembly names or IDs (but see description)
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get list of changes
+
+  Return the change log in json format. Note that when an assembly is deleted the
+  link between common name and ID is lost (it can still be recovered by inspecting
+  the change log but at present this task is left to the user). In such cases you
+  need to use the assembly ID.
+```
+
+_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/change/get.ts)_
+
+## `apollo config [KEY] [VALUE]`
+
+Get or set apollo configuration options
+
+```
+USAGE
+  $ apollo config [KEY] [VALUE] [--profile <value>] [---file <value>] [--get-config-file]
+
+ARGUMENTS
+  KEY    Name of configuration parameter
+  VALUE  Parameter value
+
+FLAGS
+  --config-file=<value>  Use this config file (mostly for testing)
+  --get-config-file      Return the path to the config file and exit (this file may not exist yet)
+  --profile=<value>      Profile to create or edit
+
+DESCRIPTION
+  Get or set apollo configuration options
+
+  Use this command to create or edit a user profile with credentials to access
+  Apollo. Configuration options are:
+
+  - address:
+  Address and port e.g http://localhost:3999
+
+  - accessType:
+  How to access Apollo. accessType is typically one of: google, microsoft, guest,
+  root. Allowed types depend on your Apollo setup
+
+  - accessToken:
+  Access token. Usually inserted by `apollo login`
+
+  - rootCredentials.username:
+  Username of root account. Only set this for "root" access type
+
+  - rootCredentials.password:
+  Password for root account. Only set this for "root" access type
+
+EXAMPLES
+  Interactive setup:
+
+    $ apollo config
+
+  Setup with key/value pairs:
+
+    $ apollo config --profile admin address http://localhost:3999
+
+  Get current address for default profile:
+
+    $ apollo config address
+```
+
+_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/config.ts)_
+
+## `apollo feature add-child`
+
+Add a child feature (e.g. add an exon to an mRNA)
+
+```
+USAGE
+  $ apollo feature add-child -s <value> -e <value> -t <value> [--profile <value>] [--config-file <value>] [-i <value>]
+
+FLAGS
+  -e, --end=<value>          (required) End coordinate of the child feature (1-based)
+  -i, --feature-id=<value>   [default: -] Add a child to this feature ID; use - to read it from stdin
+  -s, --start=<value>        (required) Start coordinate of the child feature (1-based)
+  -t, --type=<value>         (required) Type of child feature
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Add a child feature (e.g. add an exon to an mRNA)
+
+  See the other commands under `apollo feature` to retrive the parent ID of
+  interest and to populate the child feature with attributes.
+
+EXAMPLES
+  Add an exon at genomic coordinates 10..20 to this feature ID:
+
+    $ apollo feature add-child -i 6605826fbd0eee691f83e73f -t exon -s 10 -e 20
+```
+
+_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/add-child.ts)_
+
+## `apollo feature check`
+
+Get check results
+
+```
+USAGE
+  $ apollo feature check [--profile <value>] [--config-file <value>] [-i <value>] [-a <value>]
+
+FLAGS
+  -a, --assembly=<value>       Get checks for this assembly
+  -i, --feature-id=<value>...  Get checks for these feature identifiers
+      --config-file=<value>    Use this config file (mostly for testing)
+      --profile=<value>        Use credentials from this profile
+
+DESCRIPTION
+  Get check results
+
+  Use this command to view which features fail checks along with the reason for
+  failing. Use `apollo assembly check` for managing which checks should be applied
+  to an assembly
+
+EXAMPLES
+  Get all check results in the database:
+
+    $ apollo feature check
+
+  Get check results for assembly hg19:
+
+    $ apollo feature check -a hg19
+```
+
+_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/check.ts)_
+
+## `apollo feature copy`
+
+Copy a feature to another location
+
+```
+USAGE
+  $ apollo feature copy -r <value> -s <value> [--profile <value>] [--config-file <value>] [-i <value>] [-a <value>]
+
+FLAGS
+  -a, --assembly=<value>     Name or ID of target assembly. Not required if refseq is unique in the database
+  -i, --feature-id=<value>   [default: -] Feature ID to copy to; use - to read it from stdin
+  -r, --refseq=<value>       (required) Name or ID of target reference sequence
+  -s, --start=<value>        (required) Start position in target reference sequence
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Copy a feature to another location
+
+  The feature may be copied to the same or to a different assembly. he destination
+  reference sequence may be selected by name only if unique in the database or by
+  name and assembly or by identifier.
+
+EXAMPLES
+  Copy this feature ID to chr1:100 in assembly hg38:
+
+    $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38
+```
+
+_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/copy.ts)_
+
+## `apollo feature delete`
+
+Delete one or more features by ID
+
+```
+USAGE
+  $ apollo feature delete [--profile <value>] [--config-file <value>] [-i <value>] [-f] [-n]
+
+FLAGS
+  -f, --force                  Ignore non-existing features
+  -i, --feature-id=<value>...  [default: -] Feature IDs to delete
+  -n, --dry-run                Only show what would be delete
+      --config-file=<value>    Use this config file (mostly for testing)
+      --profile=<value>        Use credentials from this profile
+
+DESCRIPTION
+  Delete one or more features by ID
+
+  Note that deleting a child feature after deleting its parent will result in an
+  error unless you set -f/--force.
+```
+
+_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/delete.ts)_
+
+## `apollo feature edit`
+
+Edit features using an appropiate json input
+
+```
+USAGE
+  $ apollo feature edit [--profile <value>] [--config-file <value>] [-j <value>]
+
+FLAGS
+  -j, --json-input=<value>   [default: -] Json string or json file or "-" to read json from stdin
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Edit features using an appropiate json input
+
+  Edit a feature by submitting a json input with all the required attributes for
+  Apollo to process it. This is a very low level command which most users probably
+  do not need.
+
+  Input may be a json string or a json file and it may be an array of changes.
+  This is an example input for editing feature type:
+
+  {
+  "typeName": "TypeChange",
+  "changedIds": [
+  "6613f7d22c957525d631b1cc"
+  ],
+  "assembly": "6613f7d1360321540a11e5ed",
+  "featureId": "6613f7d22c957525d631b1cc",
+  "oldType": "BAC",
+  "newType": "G_quartet"
+  }
+
+EXAMPLES
+  Editing by passing a json to stdin:
+
+    echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j -
+```
+
+_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/edit.ts)_
+
+## `apollo feature edit-attribute`
+
+Add, edit, or view a feature attribute
+
+```
+USAGE
+  $ apollo feature edit-attribute -a <value> [--profile <value>] [--config-file <value>] [-i <value>] [-v <value>] [-d]
+
+FLAGS
+  -a, --attribute=<value>    (required) Attribute key to add or edit
+  -d, --delete               Delete this attribute
+  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
+  -v, --value=<value>...     New attribute value. Separated mutliple values by space to them as a list. If unset return
+                             current value
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Add, edit, or view a feature attribute
+
+  Be aware that there is no checking whether attributes names and values are
+  valid. For example, you can create non-unique ID attributes or you can set gene
+  ontology terms to non-existing terms
+
+EXAMPLES
+  Add attribute "domains" with a list of values:
+
+    $ apollo feature edit-attribute -i 66...3f -a domains -v ABC PLD
+
+  Print values in "domains" as json array:
+
+    $ apollo feature edit-attribute -i 66...3f -a domains
+
+  Delete attribute "domains"
+
+    $ apollo feature edit-attribute -i 66...3f -a domains -d
+```
+
+_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+
+## `apollo feature edit-coords`
+
+Edit feature start and/or end coordinates
+
+```
+USAGE
+  $ apollo feature edit-coords [--profile <value>] [--config-file <value>] [-i <value>] [-s <value>] [-e <value>]
+
+FLAGS
+  -e, --end=<value>          New end coordinate (1-based)
+  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
+  -s, --start=<value>        New start coordinate (1-based)
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Edit feature start and/or end coordinates
+
+  If editing a child feature that new coordinates must be within the parent's
+  coordinates. To get the identifier of the feature to edit consider using `apollo
+  feature get` or `apollo feature search`
+
+EXAMPLES
+  Edit start and end:
+
+    $ apollo feature edit-coords -i abc...xyz -s 10 -e 1000
+
+  Edit end and leave start as it is:
+
+    $ apollo feature edit-coords -i abc...xyz -e 2000
+```
+
+_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+
+## `apollo feature edit-type`
+
+Edit or view feature type
+
+```
+USAGE
+  $ apollo feature edit-type [--profile <value>] [--config-file <value>] [-i <value>] [-t <value>]
+
+FLAGS
+  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
+  -t, --type=<value>         Assign feature to this type. If unset return the current type
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Edit or view feature type
+
+  Feature type is column 3 in gff format. It must be a valid sequence ontology
+  term although but the valifdity of the new term is not checked.
+```
+
+_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+
+## `apollo feature get`
+
+Get features in assembly, reference sequence or genomic window
+
+```
+USAGE
+  $ apollo feature get [--profile <value>] [--config-file <value>] [-a <value>] [-r <value>] [-s <value>] [-e
+    <value>]
+
+FLAGS
+  -a, --assembly=<value>     Find input reference sequence in this assembly
+  -e, --end=<value>          End coordinate
+  -r, --refseq=<value>       Reference sequence. If unset, query all sequences
+  -s, --start=<value>        [default: 1] Start coordinate (1-based)
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get features in assembly, reference sequence or genomic window
+
+EXAMPLES
+  Get all features in myAssembly:
+
+    $ apollo feature get -a myAssembly
+
+  Get features intersecting chr1:1..1000. You can omit the assembly name if there
+  are no other reference sequences named chr1:
+
+    $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000
+```
+
+_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/get.ts)_
+
+## `apollo feature get-id`
+
+Get features given their identifiers
+
+```
+USAGE
+  $ apollo feature get-id [--profile <value>] [--config-file <value>] [-i <value>]
+
+FLAGS
+  -i, --feature-id=<value>...  [default: -] Retrieves feature with these IDs. Use
+                               "-" to read IDs from stdin (one per
+                               line)
+      --config-file=<value>    Use this config file (mostly for testing)
+      --profile=<value>        Use credentials from this profile
+
+DESCRIPTION
+  Get features given their identifiers
+
+  Invalid identifiers or identifiers not found in the database will be silently
+  ignored
+
+EXAMPLES
+  Get features for these identifiers:
+
+    $ apollo feature get-id -i abc...zyz def...foo
+```
+
+_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/get-id.ts)_
+
+## `apollo feature import`
+
+Import features from local gff file
+
+```
+USAGE
+  $ apollo feature import -i <value> -a <value> [--profile <value>] [--config-file <value>] [-d]
+
+FLAGS
+  -a, --assembly=<value>     (required) Import into this assembly name or assembly ID
+  -d, --delete-existing      Delete existing features before importing
+  -i, --input-file=<value>   (required) Input gff or gtf file
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Import features from local gff file
+
+  By default, features are added to the existing ones.
+
+EXAMPLES
+  Delete features in myAssembly and then import features.gff3:
+
+    $ apollo feature import -d -i features.gff3 -a myAssembly
+```
+
+_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/import.ts)_
+
+## `apollo feature search`
+
+Free text search for feature in one or more assemblies
+
+```
+USAGE
+  $ apollo feature search -t <value> [--profile <value>] [--config-file <value>] [-a <value>]
+
+FLAGS
+  -a, --assembly=<value>...  Assembly names or IDs to search; use "-" to read it from stdin. If omitted
+                             search all assemblies
+  -t, --text=<value>         (required) Search for this text query
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Free text search for feature in one or more assemblies
+
+  Return features matching a query string. This command searches only in:
+
+  - Attribute *values* (not attribute names)
+  - Source field (which in fact is stored as an attribute)
+  - Feature type
+
+  The search mode is:
+
+  - Case insensitive
+  - Match only full words, but not necessarily the full value
+  - Common words are ignored. E.g. "the", "with"
+
+  For example, given this feature:
+
+  chr1 example SNP 10 30 0.987 . . "someKey=Fingerprint BAC with reads"
+
+  Queries "bac" or "mRNA" return the feature. Instead these queries will NOT
+  match:
+
+  - "someKey"
+  - "with"
+  - "Finger"
+  - "chr1"
+  - "0.987"
+
+EXAMPLES
+  Search "bac" in these assemblies:
+
+    $ apollo feature search -a mm9 mm10 -t bac
+```
+
+_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/feature/search.ts)_
+
+## `apollo help [COMMANDS]`
+
+Display help for apollo.
+
+```
+USAGE
+  $ apollo help [COMMANDS] [-n]
+
+ARGUMENTS
+  COMMANDS  Command to show help for.
+
+FLAGS
+  -n, --nested-commands  Include all nested commands in the output.
+
+DESCRIPTION
+  Display help for apollo.
+```
+
+_See code: [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
+
+## `apollo login`
+
+Login to Apollo
+
+```
+USAGE
+  $ apollo login [--profile <value>] [--config-file <value>] [-a <value>] [-u <value>] [-p <value>] [-f]
+    [--port <value>]
+
+FLAGS
+  -a, --address=<value>      Address of Apollo server
+  -f, --force                Force re-authentication even if user is already logged in
+  -p, --password=<value>     Password for <username>
+  -u, --username=<value>     Username for root login
+      --config-file=<value>  Use this config file (mostly for testing)
+      --port=<value>         [default: 3000] Get token by listening to this port number (usually this is >= 1024 and <
+                             65536)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Login to Apollo
+
+  Use the provided credentials to obtain and save the token to access Apollo. Once
+  the token for the given profile has been saved in the configuration file, users
+  do not normally need to execute this command again unless the token has expired.
+  To setup a new profile use "apollo config"
+
+EXAMPLES
+  The most basic and probably most typical usage is to login using the default
+  profile in configuration file:
+
+    $ apollo login
+
+  Login with a different profile:
+
+    $ apollo login --profile my-profile
+```
+
+_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/login.ts)_
+
+## `apollo logout`
+
+Logout of Apollo
+
+```
+USAGE
+  $ apollo logout [--profile <value>] [--config-file <value>]
+
+FLAGS
+  --config-file=<value>  Use this config file (mostly for testing)
+  --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Logout of Apollo
+
+  Logout by removing the access token from the selected profile
+
+EXAMPLES
+  Logout default profile:
+
+    $ apollo logout
+
+  Logout selected profile
+
+    $ apollo logout --profile my-profile
+```
+
+_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/logout.ts)_
+
+## `apollo refseq get`
+
+Get reference sequences
+
+```
+USAGE
+  $ apollo refseq get [--profile <value>] [--config-file <value>] [-a <value>]
+
+FLAGS
+  -a, --assembly=<value>...  Get reference sequences for these assembly names or IDs; use - to read it from stdin
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get reference sequences
+
+  Output the reference sequences in one or more assemblies in json format. This
+  command returns the sequence characteristics (e.g., name, ID, etc), not the DNA
+  sequences. Use `assembly sequence` for that.
+
+EXAMPLES
+  All sequences in the database:
+
+    $ apollo refseq get
+
+  Only sequences for these assemblies:
+
+    $ apollo refseq get -a mm9 mm10
+```
+
+_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/refseq/get.ts)_
+
+## `apollo status`
+
+View authentication status
+
+```
+USAGE
+  $ apollo status [--profile <value>] [--config-file <value>]
+
+FLAGS
+  --config-file=<value>  Use this config file (mostly for testing)
+  --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  View authentication status
+
+  This command returns "<profile>: Logged in" if the selected profile has an
+  access token and "<profile>: Logged out" otherwise. Note that this command does
+  not check the validity of the access token.
+```
+
+_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/status.ts)_
+
+## `apollo user get`
+
+Get list of users
+
+```
+USAGE
+  $ apollo user get [--profile <value>] [--config-file <value>] [-u <value>] [-r <value>]
+
+FLAGS
+  -r, --role=<value>         Get users with this role
+  -u, --username=<value>     Find this username
+      --config-file=<value>  Use this config file (mostly for testing)
+      --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get list of users
+
+  If set, filters username and role must be both satisfied to return an entry
+
+EXAMPLES
+  By username:
+
+    $ apollo user get -u Guest
+
+  By role:
+
+    $ apollo user get -r admin
+
+  Use jq for more control:
+
+    $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")'
+```
+
+_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.10/packages/apollo-cli/src/commands/user/get.ts)_
+<!-- commandsstop -->